Functional groups
Sequence pre-processing
Summary statistics for each of the functional groups declared in the app.
The app includes the P1 and P11 naive datasets, and P3, P4, P7, P8, P9 non-naive dataset.
For all projects the following filtration criteria were applied:
- Functional sequence, no stop codons or frame shifts.
- Sequences which start from position 1 of the V gene.
- Sequences which didn’t have gaps open (-) and didn’t include any N’s
- After changing into group annotations, sequences which had more than a single assignment in naive repertoires were remove.
For the non naive datasets only IGM/IGD sequences were taken and the V region was filtered to up to 3 mutations.
The groups were created with similarity of 95% based on complete linkage and functional sequences and up to position 318.
Groups Repertoire normalization
The current groups threshold and the possible states are in the table below.
Going over the groups showed several thins
- We saw potential duplication events, such as in the case of IGHV1-69*04 in sample P1_I50 from group G8, where we think this allele might be sitting in the duplicated gene.
- An interesting event involving a duplicated gene is in the case of IGHV3-43D from group G22. In this group 5 alleles are present, where three alleles are supposedly from the duplicated gene. Allele D*04 and D*04_G4A goes in states two with allele 01, in the J6 heterozygous samples we saw a double single chromosome deletion event. This occurred in 7 individuals and raises the question if maybe both alleles are sitting in the same location on the chromosome and are not acutely deleted.
- Group 19 and genes IGHV3-23 and IGHV3-23D, showed a very low usage for the D gene.
- From the usage results, we suspect that the gene in IGHV3-35G21 might be a pseudo gene.
- We saw several signle chromosome deletion events in gene V3-66 from the group G25, which also has the gene V3-53.
- In the group IGHV3-64G27, we suspect that allele 3-64*02 might be a pseudo allele due to very low usage.
- In group G34 there are only two states, and include two genes. In state one only an allele from V4-30-2 appears. While in state 2, one allele V4-30-2 and one from V4-30-4 appears.
- In group G48 there is a novel allele V6-1*01_T91C. This allele only appears in state 2 and is lowly expressed, much more when the max mutation value is 0.
Based on the threshold we compared the alleles present in IMGT versus those that passed the threshold.
We plotted the relative repertoire plotted. Each dot is an individual and the colors shows the zygousity state while the shape indicates the project.
IGHV1-18 - G1
Allele appearnce
The group of IGHV1-18 includes 3 alleles, 3 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewed alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.01\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 2 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV1-2 - G2
Allele appearnce
The group of IGHV1-2 includes 7 alleles, 7 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.01\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 3 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV1-24 - G3
Allele appearnce
The group of IGHV1-24 includes 1 alleles, 1 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Observations
For this group we’ve seen a single allele, hence the general summary statistics do not apply here and were omitted.
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Conclusions
Because we observed a single allele in this group we set the cutoff to \(0.01%\) absolute threshold (the relative repertoire frequency). The plot below shows the frequency of the group above the threshold line.
IGHV1-3 - G4
Allele appearnce
The group of IGHV1-3 includes 5 alleles, 5 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.01\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 3 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV1-45 - G5
Allele appearnce
The group of IGHV1-45 includes 3 alleles, 3 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 3 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV1-46 - G6
Allele appearnce
The group of IGHV1-46 includes 4 alleles, 4 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.01\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 2 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV1-58 - G7
Allele appearnce
The group of IGHV1-58 includes 3 alleles, 3 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 2 zygousity states.
Observations
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Conclusions
Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV1-69-2 - G8
No rearrangements were found from this group
IGHV1-69D/IGHV1-69 - G9
Allele appearnce
The group of IGHV1-69/IGHV1-69D includes 20 alleles, 20 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
Observations
For this group we’ve seen a single allele, hence the general summary statistics do not apply here and were omitted.
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV1-8 - G10
Allele appearnce
The group of IGHV1-8 includes 3 alleles, 3 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 2 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV2-26 - G11
Allele appearnce
The group of IGHV2-26 includes 4 alleles, 4 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 2 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV2-5 - G12
Allele appearnce
The group of IGHV2-5 includes 6 alleles, 6 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 2 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV2-70D/IGHV2-70 - G13
Allele appearnce
The group of IGHV2-70/IGHV2-70D includes 15 alleles, 15 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 4 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV3-11 - G14
Allele appearnce
The group of IGHV3-11 includes 5 alleles, 5 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 2 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV3-13 - G15
Allele appearnce
The group of IGHV3-13 includes 5 alleles, 5 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 3 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV3-15 - G16
Allele appearnce
The group of IGHV3-15 includes 10 alleles, 10 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 2 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV3-20 - G17
Allele appearnce
The group of IGHV3-20 includes 2 alleles, 2 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 2 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV3-21 - G18
Allele appearnce
The group of IGHV3-21 includes 7 alleles, 7 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 2 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV3-23D/IGHV3-23 - G19
Allele appearnce
The group of IGHV3-23/IGHV3-23D includes 6 alleles, 6 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 3 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV3-30-5/IGHV3-30/IGHV3-33/IGHV3-30-3 - G20
Allele appearnce
The group of IGHV3-30-3/IGHV3-30-5/IGHV3-30/IGHV3-33 includes 35 alleles, 35 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 7 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV3-35 - G21
Allele appearnce
The group of IGHV3-35 includes 1 alleles, 1 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Observations
For this group we’ve seen a single allele, hence the general summary statistics do not apply here and were omitted.
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Conclusions
IGHV3-43D/IGHV3-43 - G22
Allele appearnce
The group of IGHV3-43/IGHV3-43D includes 5 alleles, 5 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 5 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV3-48 - G23
Allele appearnce
The group of IGHV3-48 includes 4 alleles, 4 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 3 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV3-49 - G24
Allele appearnce
The group of IGHV3-49 includes 5 alleles, 5 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 3 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV3-66/IGHV3-53 - G25
Allele appearnce
The group of IGHV3-53/IGHV3-66 includes 11 alleles, 11 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 4 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV3-62 - G26
Allele appearnce
The group of IGHV3-62 includes 1 alleles, 1 out of the alleles are functional.
No rearrangments were found for this group, hence the general summary statistics do not apply here and were omitted. ## Observations
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Conclusions
IGHV3-64D/IGHV3-64 - G27
Allele appearnce
The group of IGHV3-64/IGHV3-64D includes 9 alleles, 9 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 4 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV3-7 - G28
Allele appearnce
The group of IGHV3-7 includes 5 alleles, 5 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 3 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV3-72 - G29
Allele appearnce
The group of IGHV3-72 includes 1 alleles, 1 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Observations
For this group we’ve seen a single allele, hence the general summary statistics do not apply here and were omitted.
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV3-73 - G30
Allele appearnce
The group of IGHV3-73 includes 2 alleles, 2 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 2 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV3-74 - G31
Allele appearnce
The group of IGHV3-74 includes 3 alleles, 3 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 2 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV3-9 - G32
Allele appearnce
The group of IGHV3-9 includes 4 alleles, 4 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 3 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV4-28 - G33
Allele appearnce
The group of IGHV4-28 includes 7 alleles, 7 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 3 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV4-30-4/IGHV4-30-2 - G34
Allele appearnce
The group of IGHV4-30-2/IGHV4-30-4 includes 6 alleles, 6 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 1 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV4-31/IGHV4-30-4 - G35
Allele appearnce
The group of IGHV4-30-4/IGHV4-31 includes 9 alleles, 9 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 4 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV4-34 - G36
Allele appearnce
The group of IGHV4-34 includes 6 alleles, 6 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 2 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV4-34 - G37
Allele appearnce
There are no rearrangments for this group.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
IGHV4-34 - G37
Allele appearnce
There are no rearrangments for this group.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
IGHV4-39/IGHV4-38-2 - G38
Allele appearnce
The group of IGHV4-38-2/IGHV4-39 includes 10 alleles, 10 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 5 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV4-4 - G39
Allele appearnce
The group of IGHV4-4 includes 4 alleles, 4 out of the alleles are functional.
For this group we have not seen any rearrangements. Hence, no concrete conclusion can be drawn
IGHV4-59/IGHV4-4 - G40
Allele appearnce
The group of IGHV4-4/IGHV4-59 includes 2 alleles, 2 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
## NULL
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 2 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV4-59/IGHV4-4 - G41
Allele appearnce
The group of IGHV4-4/IGHV4-59 includes 10 alleles, 10 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 4 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV4-61 - G42
Allele appearnce
The group of IGHV4-61 includes 9 alleles, 9 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 3 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV5-10-1 - G43
Allele appearnce
The group of IGHV5-10-1 includes 4 alleles, 4 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 2 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV5-51 - G44
Allele appearnce
The group of IGHV5-51 includes 6 alleles, 6 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 4 zygousity states.
Observations
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Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.
Allele specific cutoff
IGHV6-1 - G45
Allele appearnce
Allele appearnce
There are no rearrangements for this group. A single allele appear in this group, IGHV4-59G45*06
IGHV7-4-1 - G46
Allele appearnce
The group of IGHV7-4-1 includes 4 alleles, 4 out of the alleles are functional.
For each allele we counted the number of appearances across the population, any appearance was considered valid.
Group alignment
Based on the viewd alleles, we calculated the distance between the germline sequences.
Sequence depth
To examine the potential cutoff we observed the sequence depth for each allele
Absolute cutoff
We set an initial cutoff of \(0.5\%\) to determine the potential genotype priors. For this cutoff we examined the zygousity state, such as homozygousity, heterozygousity and so on.
With the selected cutoff we saw that there are 3 zygousity states.
Observations
This section is editable by clicking on the edit button below. To refresh the section click on the refresh button
You can access the file also from here
Conclusions
From the results we believe that the cutoff for this group should be
and for the adjusted states the allele combinations and the relations are stated in the table below.